Genomics technology has paved the way for a global and unbiased quantitative and qualitative assessment of the immune response. We have developed an Immune Array platform based on whole genome microarray analysis and a transcriptomic approach that is well suited to identify the mechanisms that lead to protective immunity induced by vaccines. We have previously used this platform to describe the very early induction (3 to 7 days) of a network of transcription factors that precede the development of highly integrated innate and adaptive immune responses induced by the Yellow Fever vaccine. In the Systems Biology Core E of this consortium, we aim to (i) provide a centralized sample, reporting, and data management and distribution framework, (ii) perform a comprehensive systems biology assessment of SIV vector-mediated innate and adaptive immune responses, (iii) provide rigorous biostatistical processing and power analysis of microarray and quantitative RT-PCR (QPCR) analysis, and (iv) provide projects and core-integrated immune correlate analysis for SIV vector immune characterization, selection, and study. The aims of the core will be met via our commercial grade Laboratory Information Management System (LIMS), our SOP-driven, high-throughput. Immune Array platform for microarray analysis, our standardized, semiautomated bioinformatic reporting, and our template-driven data mapping of biological contexts/outcomes to integrate multiple projects and multiple OMIC platforms. We will use these leading edge technologies and bioinformatic strategies to assess the transcriptomic signatures that define early SIV-mediated host responses following different routes of mucosal challenge and the impact of SIV vector-mediated protection.